Mercurial > repos > jjohnson > defuse
view defuse_trinity_analysis.py @ 39:90127ee1eae5
Fix defuse_trinity_analysis.py
author | Jim Johnson <jj@umn.edu> |
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date | Thu, 12 Feb 2015 06:54:38 -0600 |
parents | 4353f776dfa3 |
children | ed07bcc39f6e |
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#!/usr/bin/env python """ # #------------------------------------------------------------------------------ # University of Minnesota # Copyright 2014, Regents of the University of Minnesota #------------------------------------------------------------------------------ # Author: # # James E Johnson # #------------------------------------------------------------------------------ """ """ This tool takes the defuse results.tsv tab-delimited file, trinity and creates a tabular report """ import sys,re,os.path import optparse from optparse import OptionParser revcompl = lambda x: ''.join([{'A':'T','C':'G','G':'C','T':'A','a':'t','c':'g','g':'c','t':'a','N':'N','n':'n'}[B] for B in x][::-1]) def read_fasta(fp): name, seq = None, [] for line in fp: line = line.rstrip() if line.startswith(">"): if name: yield (name, ''.join(seq)) name, seq = line, [] else: seq.append(line) if name: yield (name, ''.join(seq)) def test_rcomplement(seq, target): try: comp = revcompl(seq) return comp in target except: pass return False def test_reverse(seq,target): return options.test_reverse and seq and seq[::-1] in target def cmp_alphanumeric(s1,s2): if s1 == s2: return 0 a1 = re.findall("\d+|[a-zA-Z]+",s1) a2 = re.findall("\d+|[a-zA-Z]+",s2) for i in range(min(len(a1),len(a2))): if a1[i] == a2[i]: continue if a1[i].isdigit() and a2[i].isdigit(): return int(a1[i]) - int(a2[i]) return 1 if a1[i] > a2[i] else -1 return len(a1) - len(a2) def parse_defuse_results(inputFile): columns = [] defuse_results = [] # {cluster_id : { field : value}) try: for linenum,line in enumerate(inputFile): ## print >> sys.stderr, "%d: %s\n" % (linenum,line) fields = line.strip().split('\t') if line.startswith('cluster_id'): columns = fields ## print >> sys.stderr, "columns: %s\n" % columns continue cluster_dict = dict() cluster_id = fields[columns.index('cluster_id')] cluster_dict['cluster_id'] = fields[columns.index('cluster_id')] cluster_dict['gene_chromosome1'] = fields[columns.index('gene_chromosome1')] cluster_dict['gene_chromosome2'] = fields[columns.index('gene_chromosome2')] cluster_dict['genomic_strand1'] = fields[columns.index('genomic_strand1')] cluster_dict['genomic_strand2'] = fields[columns.index('genomic_strand2')] cluster_dict['gene1'] = fields[columns.index('gene1')] cluster_dict['gene2'] = fields[columns.index('gene2')] cluster_dict['gene_name1'] = fields[columns.index('gene_name1')] cluster_dict['gene_name2'] = fields[columns.index('gene_name2')] cluster_dict['gene_location1'] = fields[columns.index('gene_location1')] cluster_dict['gene_location2'] = fields[columns.index('gene_location2')] cluster_dict['expression1'] = int(fields[columns.index('expression1')]) cluster_dict['expression2'] = int(fields[columns.index('expression2')]) cluster_dict['genomic_break_pos1'] = int(fields[columns.index('genomic_break_pos1')]) cluster_dict['genomic_break_pos2'] = int(fields[columns.index('genomic_break_pos2')]) cluster_dict['breakpoint_homology'] = int(fields[columns.index('breakpoint_homology')]) cluster_dict['orf'] = fields[columns.index('orf')] == 'Y' cluster_dict['exonboundaries'] = fields[columns.index('exonboundaries')] == 'Y' cluster_dict['read_through'] = fields[columns.index('read_through')] == 'Y' cluster_dict['interchromosomal'] = fields[columns.index('interchromosomal')] == 'Y' cluster_dict['adjacent'] = fields[columns.index('adjacent')] == 'Y' cluster_dict['altsplice'] = fields[columns.index('altsplice')] == 'Y' cluster_dict['deletion'] = fields[columns.index('deletion')] == 'Y' cluster_dict['eversion'] = fields[columns.index('eversion')] == 'Y' cluster_dict['inversion'] = fields[columns.index('inversion')] == 'Y' cluster_dict['span_count'] = int(fields[columns.index('span_count')]) cluster_dict['splitr_count'] = int(fields[columns.index('splitr_count')]) cluster_dict['splice_score'] = int(fields[columns.index('splice_score')]) cluster_dict['probability'] = float(fields[columns.index('probability')] if columns.index('probability') else 'nan') cluster_dict['splitr_sequence'] = fields[columns.index('splitr_sequence')] defuse_results.append(cluster_dict) except Exception, e: print >> sys.stderr, "failed: %s" % e sys.exit(1) return defuse_results ## deFuse params to the mapping application? def __main__(): #Parse Command Line parser = optparse.OptionParser() # files parser.add_option( '-i', '--input', dest='input', help='The input defuse results.tsv file (else read from stdin)' ) parser.add_option( '-t', '--transcripts', dest='transcripts', default=None, help='Trinity transcripts' ) parser.add_option( '-p', '--peptides', dest='peptides', default=None, help='Trinity ORFs' ) parser.add_option( '-o', '--output', dest='output', help='The output report (else write to stdout)' ) parser.add_option( '-a', '--transcript_alignment', dest='transcript_alignment', help='The output alignment file' ) parser.add_option( '-A', '--orf_alignment', dest='orf_alignment', help='The output alignment file' ) parser.add_option( '-N', '--nbases', dest='nbases', type='int', default=12, help='Number of bases on either side of the fusion to compare' ) parser.add_option( '-L', '--min_pep_len', dest='min_pep_len', type='int', default=100, help='Minimum length of peptide to report' ) parser.add_option( '-T', '--ticdist', dest='ticdist', type='int', default=1000000, help='Maximum intrachromosomal distance to be classified a Transcription-induced chimera (TIC)' ) parser.add_option( '-P', '--prior_aa', dest='prior_aa', type='int', default=11, help='Number of protein AAs to show preceeding fusion point' ) # min_orf_len # split_na_len # tic_len = 1000000 # prior # deFuse direction reversed # in frame ? # contain known protein elements # what protein change # trinity provides full transctipt, defuse doesn't show full #parser.add_option( '-r', '--reference', dest='reference', default=None, help='The genomic reference fasta' ) #parser.add_option( '-g', '--gtf', dest='gtf', default=None, help='The genomic reference gtf feature file') (options, args) = parser.parse_args() # results.tsv input if options.input != None: try: inputPath = os.path.abspath(options.input) inputFile = open(inputPath, 'r') except Exception, e: print >> sys.stderr, "failed: %s" % e exit(2) else: inputFile = sys.stdin # vcf output if options.output != None: try: outputPath = os.path.abspath(options.output) outputFile = open(outputPath, 'w') except Exception, e: print >> sys.stderr, "failed: %s" % e exit(3) else: outputFile = sys.stdout ## Read defuse results fusions = parse_defuse_results(inputFile) ## Create a field with the 12 nt before and after the fusion point. ## Create a field with the reverse complement of the 24 nt fusion point field. ## Add fusion type filed (INTER, INTRA, TIC) for i,fusion in enumerate(fusions): fusion['ordinal'] = i + 1 split_seqs = fusion['splitr_sequence'].split('|') fusion['split_seqs'] = split_seqs fwd_seq = split_seqs[0][-(min(abs(options.nbases),len(split_seqs[0]))):] + split_seqs[1][:min(abs(options.nbases),len(split_seqs[1]))] rev_seq = revcompl(fwd_seq) fusion['fwd_seq'] = fwd_seq fusion['rev_seq'] = rev_seq fusion_type = 'inter' if fusion['gene_chromosome1'] != fusion['gene_chromosome2'] else 'intra' if abs(fusion['genomic_break_pos1'] - fusion['genomic_break_pos2']) > options.ticdist else 'TIC' fusion['fusion_type'] = fusion_type fusion['transcripts'] = [] fusion['Transcript'] = 'No' fusion['Protein'] = 'No' #print >> sys.stdout, "%4d\t%6s\t%s\t%s\t%s\t%s\t%s" % (i,fusion['cluster_id'],fwd_seq,rev_seq,fusion_type,fusion['gene_name1'],fusion['gene_name2']) inputFile.close() ## Process Trinity data and compare to deFuse matched_transcripts = dict() matched_orfs = dict() fusions_with_transcripts = set() fusions_with_orfs = set() n = 0 if options.transcripts: with open(options.transcripts) as fp: for name, seq in read_fasta(fp): n += 1 for i,fusion in enumerate(fusions): if fusion['fwd_seq'] in seq or fusion['rev_seq'] in seq: fusions_with_transcripts.add(i) matched_transcripts[name] = seq fusion['transcripts'].append(name) fusion['Transcript'] = 'Yes' #print >> sys.stdout, "fusions_with_transcripts: %d %s\n matched_transcripts: %d" % (len(fusions_with_transcripts),fusions_with_transcripts,len(matched_transcripts)) print >> sys.stdout, "fusions_with_transcripts: %d unique_transcripts: %d" % (len(fusions_with_transcripts),len(matched_transcripts)) #for i,fusion in enumerate(fusions): # print >> sys.stdout, "%4d\t%6s\t%s\t%s\t%s\t%s\t%s\t%s" % (i,fusion['cluster_id'],fusion['fwd_seq'],fusion['rev_seq'],fusion['fusion_type'],fusion['gene_name1'],fusion['gene_name2'], fusion['transcripts']) ## Process ORFs and compare to matched deFuse and Trinity data. ## Proteins must be at least 100 aa long, starting at the first "M" and must end with an "*". if options.peptides: with open(options.peptides) as fp: for name, seq in read_fasta(fp): n += 1 if len(seq) < options.min_pep_len: continue for i,fusion in enumerate(fusions): if len(fusion['transcripts']) > 0: for id_string in fusion['transcripts']: tx_id = id_string.lstrip('>').split()[0] if tx_id in name: pep_len = len(seq) start = seq.find('M') if pep_len - start < options.min_pep_len: continue fusions_with_orfs.add(i) matched_orfs[name] = seq fusion['Protein'] = 'Yes' """ # fwd or reverse tx_seq = matched_transcripts(tx_id) pos = tx_seq.find(fusion['fwd_seq']) if pos < 0: pos = tx_seq.find(fusion['rev_seq']) # locate fusion in transcript # locate fusion in ORF fusion['prior_pep_seq'] = '' fusion['novel_pep_seq'] = '' """ #print >> sys.stdout, "fusions_with_orfs: %d %s\n matched_orfs: %d" % (len(fusions_with_orfs),fusions_with_orfs,len(matched_orfs)) print >> sys.stdout, "fusions_with_orfs: %d unique_orfs: %d" % (len(fusions_with_orfs),len(matched_orfs)) ## Write reports report_fields = ['gene_name1','gene_name2','span_count','probability','gene_chromosome1','gene_location1','gene_chromosome2','gene_location2','fusion_type','Transcript','Protein'] report_colnames = {'gene_name1':'Gene 1','gene_name2':'Gene 2','span_count':'Span cnt','probability':'Probability','gene_chromosome1':'From Chr','gene_location1':'Fusion point','gene_chromosome2':'To Chr','gene_location2':'Fusion point','fusion_type':'Type','Transcript':'Transcript?','Protein':'Protein?' } print >> outputFile,"%s\t%s" % ('#','\t'.join([report_colnames[x] for x in report_fields])) for i,fusion in enumerate(fusions): print >> outputFile,"%s\t%s" % (i + 1,'\t'.join([str(fusion[x]) for x in report_fields])) # print >> outputFile, "%d\t%s\t%s\t%d\t%f\t%s\t%s\t%s\t%s\t%s\t%s\t%s" % (i,fusion['gene_name1'],fusion['gene_name2'],fusion['span_count'],fusion['probability'],fusion['gene_chromosome1'],fusion['gene_location1'],fusion['gene_chromosome2'],fusion['gene_location2'],fusion['fusion_type'],fusion['Transcript'],fusion['Protein']) if __name__ == "__main__" : __main__()